In order to accommodate huge number of antennas in a limited antenna size, a large scale antenna array is expected to have a three dimensional (3D) array structure. By using the Active Antenna Systems (AAS), the weights of the antenna elements arranged vertically could be configured adaptively. Then, a degree of freedom (DOF) in the vertical plane is provided for system design. So the three-dimension MIMO (3D MIMO) could be realized to solve the actual implementation problem of the massive MIMO. However, in 3D massive MIMO systems, the pilot contamination problem studied in 2D massive MIMO systems and the inter-cell interference as well as inter-vertical sector interference in 3D MIMO systems with vertical sectorization exist simultaneously, when the number of antenna is not large enough. This paper investigates the interference management towards the above challenges in 3D massive MIMO systems. Here, vertical sectorization based on vertical beamforming is included in the concerned systems. Firstly, a cooperative joint vertical beams adjustment and pilot assignment scheme is developed to improve the channel estimation precision of the uplink with pilots being reused across the vertical